This is the skeleton rmd outlining the development of a revised (“new”) QRF model (See et al. 2021). This will eventually highlight the covariate selection process, QRF model fit, the RF extrapolation model, and finally compare extrapolation estimates between the original and new models for eight watersheds within the Upper Salmon Basin.
Explain covariate selection process. DASH/resto compatible, high MIC, low correlation, missing data, lots of zeros, species specific models, and eventually converting to joint models.
Talk about relative importance and pdp plots.
Talk about GAA’s
Extrapolations of habitat capacity for Chinook salmon, by life-stage, within the North Fork Salmon watershed.
Extrapolations of habitat capacity for steelhead, by life-stage, within the North Fork Salmon watershed..
Change in predicted habitat capacity for Chinook salmon compared to the previous extrapolation, by life-stage, within the North Fork Salmon watershed.
| Model | Watershed | Predicted capacity | Capacity % change | Predicted capacity SE | SE % change |
|---|---|---|---|---|---|
| Juv summer | EF Salmon | 689,267.0 | 34 | 74,826 | 141 |
| Juv summer | Lemhi | 532,806.3 | -7 | 23,315 | 33 |
| Juv summer | NF Salmon | 184,759.5 | -5 | 16,204 | 52 |
| Juv summer | Pahsimeroi | 200,435.3 | -11 | 8,313 | -1 |
| Juv summer | Panther Cr | 505,906.7 | 4 | 41,601 | 77 |
| Juv summer | Upper Salmon | 973,874.1 | 37 | 114,743 | 120 |
| Juv summer | Valley Cr | 467,674.0 | 13 | 72,134 | 117 |
| Juv summer | Yankee Fork | 524,567.5 | 54 | 90,995 | 281 |
| Juv winter | EF Salmon | 34,428.5 | -75 | 67,228 | 388 |
| Juv winter | Lemhi | 61,977.1 | -60 | 28,701 | 325 |
| Juv winter | NF Salmon | 24,708.7 | -55 | 25,271 | 401 |
| Juv winter | Pahsimeroi | 33,654.4 | -64 | 15,138 | 123 |
| Juv winter | Panther Cr | 60,186.4 | -61 | 50,357 | 402 |
| Juv winter | Upper Salmon | 38,599.2 | -83 | 78,869 | 224 |
| Juv winter | Valley Cr | 23,612.5 | -82 | 47,311 | 256 |
| Juv winter | Yankee Fork | 29,059.3 | -71 | 65,686 | 408 |
| Redds | EF Salmon | 363.3 | -22 | 29,624 | 101,387 |
| Redds | Lemhi | 323.3 | -4 | 14,345 | 155,682 |
| Redds | NF Salmon | 151.1 | -14 | 9,143 | 112,226 |
| Redds | Pahsimeroi | 125.6 | 12 | 6,458 | 169,943 |
| Redds | Panther Cr | 392.8 | -15 | 19,546 | 101,478 |
| Redds | Upper Salmon | 517.6 | -28 | 36,800 | 76,211 |
| Redds | Valley Cr | 347.2 | -38 | 22,465 | 64,316 |
| Redds | Yankee Fork | 394.2 | -44 | 26,929 | 47,844 |
Change in predicted habitat capacity for steelhead compared o the previous extrapolation, by life-stage, within the North Fork Salmon watershed..
| Model | Watershed | Predicted capacity | Capacity % change | Predicted capacity SE | SE % change |
|---|---|---|---|---|---|
| Juv summer | EF Salmon | 225,462.7 | -40 | 30,958 | 248 |
| Juv summer | Lemhi | 294,099.9 | -26 | 19,878 | 190 |
| Juv summer | NF Salmon | 202,904.2 | -23 | 23,114 | 204 |
| Juv summer | Pahsimeroi | 148,087.9 | -32 | 9,877 | 61 |
| Juv summer | Panther Cr | 230,228.7 | -25 | 16,642 | 164 |
| Juv summer | Upper Salmon | 213,209.3 | -44 | 33,036 | 199 |
| Juv summer | Valley Cr | 154,009.8 | -45 | 23,262 | 160 |
| Juv summer | Yankee Fork | 174,368.3 | -46 | 30,533 | 405 |
| Juv winter | EF Salmon | 180,845.7 | -54 | 54,038 | 91 |
| Juv winter | Lemhi | 228,750.3 | -42 | 35,943 | 99 |
| Juv winter | NF Salmon | 163,163.2 | -48 | 38,960 | 45 |
| Juv winter | Pahsimeroi | 129,045.6 | -40 | 16,943 | 47 |
| Juv winter | Panther Cr | 205,509.7 | -35 | 25,593 | 61 |
| Juv winter | Upper Salmon | 155,401.5 | -63 | 62,129 | 90 |
| Juv winter | Valley Cr | 130,227.9 | -61 | 45,613 | 61 |
| Juv winter | Yankee Fork | 150,547.5 | -64 | 59,730 | 44 |
| Redds | EF Salmon | 367.3 | -23 | 31,276 | 113,515 |
| Redds | Lemhi | 382.3 | -5 | 22,932 | 139,872 |
| Redds | NF Salmon | 287.0 | -20 | 21,118 | 116,877 |
| Redds | Pahsimeroi | 152.4 | -22 | 12,285 | 137,702 |
| Redds | Panther Cr | 279.7 | -18 | 15,998 | 121,356 |
| Redds | Upper Salmon | 393.2 | -23 | 33,945 | 100,246 |
| Redds | Valley Cr | 311.7 | -32 | 23,919 | 86,603 |
| Redds | Yankee Fork | 393.8 | -34 | 30,994 | 96,783 |